A former boyfriend of a young bookstore clerk whose body was stuffed into a suitcase and dumped in a wooded lot in Greenwich, Conn., has been arrested in connection with her death, the police said on Tuesday.

The man, Javier da Silva, was taken into custody at his home in Queens on Monday night after he used an A.T.M. card that belonged to the victim, Valerie Reyes, 24, of New Rochelle, N.Y., the authorities said.

Mr. da Silva told detectives that on Jan. 29, Ms. Reyes fell and struck her head while they had sex at her apartment, according to a criminal complaint released Tuesday. He said he bound her hands and feet, placed tape over her mouth and put her in a suitcase before driving to “a forest” and leaving the suitcase there, the complaint states.

It was unclear from the complaint if Ms. Reyes was still alive when she was placed in the suitcase. “Javier da Silva is charged with committing a gruesome kidnapping that resulted in the death of a young woman,” Geoffrey S. Berman, the U.S. attorney in Manhattan, said.

The arrest in the case, which is being prosecuted by Mr. Berman’s office, came after dozens of interviews with witnesses and the review of hundreds of hours of surveillance footage, the Greenwich police said. Mr. da Silva, who was charged with a kidnapping resulting in death, remained in custody without bail after a brief court hearing on Tuesday in White Plains.

Ms. Reyes told her mother the night before she went missing that she feared for her life.Creditvia Norma Sanchez

Ms. Sanchez said she was aware that her daughter had recently broken up with a boyfriend, and she specifically asked if she feared him. “No,” her daughter replied. Ms. Reyes lived in the basement apartment of a home that contained several other tenants, including her father, Ms. Sanchez noted.

Ms. Reyes was a clerk at a Barnes & Noble store in Scarsdale, N.Y., but never showed up for work that Tuesday, the day Mr. da Silva said he put her in the suitcase and left her in the woods. The next day, however, she was supposedly seen in New York City. The police in New Rochelle told Ms. Sanchez that her daughter was seen on surveillance video exiting a Chase Bank branch near Radio City Music Hall in Manhattan on Jan. 30 at 6:30 a.m.

The contradiction in the police account and that of Mr. da Silva was not immediately explained on Tuesday.

Ms. Sanchez said that she had taken comfort from this apparent sighting, and believed that her daughter was seeking refuge in the safety of city crowds and would come home when she felt ready. “She was planning to stay for a while,” Ms. Sanchez recalled thinking.

But on Feb. 5, highway workers in Greenwich made a grim discovery in a wooded area beside Glenville Road, near Stillman Lane, an area dotted with large estates and “No Trespassing” signs. A suitcase in the woods contained Ms. Reyes’s body, bound at the hands and feet. The area is about 14 miles from Ms. Reyes’s apartment. When the police searched her apartment this week, they found a drawing that seems to match an image of Mr. da Silva from an account he uses on social media, according to the complaint.

Mr. da Silva is a citizen of both Portugal and Venezuela, his lawyer told a federal magistrate judge, Lisa Margaret Smith, during a hearing on Tuesday afternoon. His immigration status was unclear.

Dozens of relatives, friends, co-workers and former teachers of Ms. Reyes arrived at a funeral home in New Rochelle in the blowing snow on Tuesday to pay their respects at a wake.

“She’s very nice, very sweet,” said Alan Lopez, a friend who would often see her at work when he would buy books. “She always smiles.”